I guess I'm having trouble understanding where exactly you are having problems.
I'll give you the step by step on how I do mine so maybe you'll catch something that I do differently.
- pull the top up but leave it unlatched. Attach the rear sail panels into their channels.
-start the side windows, but only do about two inches. Slide the panel into the channel along the verticle door pillar. Then flip the bottom of the window into the horizontal channel along the body. If needed you can now pull the verticle section down so it lines up better. Finish zipping the window and repeat on the other side.
- Unclip a portion of the rear sail panels closest to the tailgate. This will give you enough room to put the rear window in. Set the rear windows bar on top of the plastic clips behind the sail panels. Start your zipper about 4 inches, then slide the bar into the clips. Finish zipping the window up. If it's cold it sometimes helps to pull the rear bow down, giving yourself a little more slack. It also helps to wax the zippers a couple of times a year.
- re-attach the sail panels then clip the header clips at the windshield. Attach the passenger and drivers side channels and then your done.
Check the nylon webbing that runs from the middle bow to the rear bow. Sometimes it will get twisted around the rear bow causing the top to not line up correctly. They should lay flat against the top.
When it's below 60* it can be a real pain in the ass, but it does stretch as it warms up.
I don't know if this is going to help or not, so good luck.